From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Aug 11 2014 - 00:33:15 CDT
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Mike Makowski
Gesendet: Montag, 11. August 2014 01:05
An: namd-l_at_ks.uiuc.edu
Betreff: Re: namd-l: Running NAMD via GROMACS topology
I suppose I should provide a bit more information:
The last line of output prior to meeting any errors is:
USING GEOMETRIC MEAN TO COMBINE L-J SIGMA PARAMETERS
(note that it said arithmetic mean before invoking vdwGeometricSigma).
Following this there are a series of lines with "ERROR" before proceeding and attempting a single simulation step with energies outputting a maximum value.
Well, what does these ERRORs contain ??
Did you minimize the system? What you observer most likely is just a bad starting structure having to high potential energy (superimposed atoms).
I hope this is clear.
Michael Makowski
University of California, Irvine
Department of Chemistry,
Chemical and Material Physics,
Irvine, CA 92617
Cell: 267 588 9865
Office: 949 824 5776
On Sun, Aug 10, 2014 at 3:44 PM, Mike Makowski <mmakowsk_at_uci.edu> wrote:
Hello NAMD community,
I'm attempting to run simulations using GROMACS topology and coordinate inputs. The coordinate input reads properly but I'm generating errors when reading in the Lennard-Jones parameters and the simulation crashes with atoms moving at very high velocities. Considering that GROMACS generally performs the geometric mean (unlike NAMD's arithmetic mean) to calculate molecular parameters, I tried applying the vdwGeometricSigma but it's not making a difference. I was also concerned that the units were incompatible so I modified the input for values in terms of angstroms but that also didn't seem to make a difference. Might there be anyone who knows how NAMD reads in GROMACS inputs and may provide more information than can be found on the NAMD website? Thanks in advance!
Best Regards,
Mike
Michael Makowski
University of California, Irvine
Department of Chemistry,
Chemical and Material Physics,
Irvine, CA 92617
Cell: 267 588 <tel:267%20588%209865> 9865
Office: 949 <tel:949%20824%205776> 824 5776
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